2B1D | pdb_00002b1d

5'-D(*GP*CP*AP*GP*AP*CP*GP*TP*CP*TP*GP*C)-3' Methionine Repressor binding site

• PDB DOI: https://doi.org/10.2210/pdb2B1D/pdb
• NAKB: 2B1D

• Classification: DNA
• Mutation(s): No 


• Deposited: 2005-09-15 Released: 2005-09-27 
• Deposition Author(s): Berman, H.M., Locasale, J.W., Napoli, A.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.284 (Depositor), 0.271 (DCC) 
• R-Value Work: 
  0.235 (Depositor), 0.229 (DCC) 
• R-Value Observed: 
  0.239 (Depositor) 

Starting Model: experimental

Literature

Signatures of protein-DNA recognition in free DNA binding sites.

Locasale, J.W., Napoli, A.A., Chen, S., Berman, H.M., Lawson, C.L.

(2009) J Mol Biology 386: 1054-1065

• PubMed: 19244617 
• DOI: https://doi.org/10.1016/j.jmb.2009.01.007
• Primary Citation Related Structures: 
  1HQ7, 2B1B, 2B1C, 2B1D


• PubMed Abstract: 
  

  One obstacle to achieving complete understanding of the principles underlying sequence-dependent recognition of DNA is the paucity of structural data for DNA recognition sequences in their free (unbound) state. Here, we carried out crystallization screening of 50 DNA duplexes containing cognate protein binding sites and obtained new crystal structures of free DNA binding sites for three distinct modes of DNA recognition: anti-parallel beta strands (MetR), helix-turn-helix motif + hinge helices (PurR), and zinc fingers (Zif268). Structural changes between free and protein-bound DNA are manifested differently in each case. The new DNA structures reveal that distinctive sequence-dependent DNA geometry dominates recognition by MetR, protein-induced bending of DNA dictates recognition by PurR, and deformability of DNA along the A-B continuum is important in recognition by Zif268. Together, our findings show that crystal structures of free DNA binding sites provide new information about the nature of protein-DNA interactions and thus lend insights towards a structural code for DNA recognition.

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Organizational Affiliation: 
• Department of Chemistry and Chemical Biology, Rutgers, State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854, USA. [e-mail]

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 22.49 kDa 
• Atom Count: 1,536 
• Modeled Residue Count: 72 
• Deposited Residue Count: 72 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*GP*CP*AP*GP*AP*CP*GP*TP*CP*TP*GP*C)-3'	A, B, C, D, E, F	12	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NCO	G [auth A], I [auth C], J [auth F]	COBALT HEXAMMINE(III) Co H18 N6 DYLMFCCYOUSRTK-UHFFFAOYSA-N
MG	H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.284 (Depositor), 0.271 (DCC) 
• R-Value Work:  0.235 (Depositor), 0.229 (DCC) 
• R-Value Observed: 0.239 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.98	α = 82.15
b = 40.346	β = 69.13
c = 40.255	γ = 81.44

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
EPMR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-09-27 
Deposition Author(s): Berman, H.M., Locasale, J.W., Napoli, A.A.

Revision History  

• Version 1.0: 2005-09-27
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description